The issue is quite a bit more complicated than that, it's a shame the article portrayed it that way... I forget how this whole story goes right now but I've heard the vet I'm currently shadowing tell it many times. (And BTW he's generally very anti-over-vaccinating: truly indoor cats don't get FeLV or even rabies, cats over 6 or 7 with known early vax history don't get FVRCP at all. And it's not exactly a vaccine, but he tells clients that dogs that don't leave Berkeley - we have no mosquitoes - don't need heartgard.) I think the issue was that the three-year rabies vaccine is the one that had the reports of fibrosarcomas at inocculation sites. He used it when it first came out, but actually saw quite a few fibrosarcoma cases so switched back to the one-year vaccine, which has less risk. There's a sub-issue, which is that the one-year vaccine was apparently up for approval for administering every three years, but the FDA wanted them to re-do all their studies with bigger sample sizes or something. The company didn't want to do that (big cost for them, plus the lives of hundreds of animals), so they settled for keeping one-year approval. (This is the reason the vet cites when he skips the rabies shot for indoor-only cats - "it's probably good for more than a year anyway.") With dogs you pretty much have to do whatever your state/county/city requires for licensing - but although the 3-year rabies vaccine is acceptable for dog licenses here, this clinic uses the yearly because of the fibrosarcoma issue.
Then there's the whole thing about the transdermal vaccine for FeLV that offers longer immunity, but is such a pain in the butt to set up and use that I know a couple vets that just refuse and give the shot instead.
I think in a lot of cases, yearly vaccinations are just a way to ensure that clients actually get their pets seen every year, and it saves the vet (or the client, particularly if you're talking about the kind of people who go to a different vet every time) having to keep track of the fact that Fluffy got her last rabies two years ago, but is due for the combo this year...
Oh, and according to this same vet the company that makes the FVRCP - not sure if it's true for the dog combo too - is considering breaking the vaccine up into three components, so that you give one shot a year but each year it's a different 3-year vaccine. While this might make medical sense from the point of view of reducing vaccine reactions by not asking the immune system to take on so much all at once, it would also have the attractive side effect of requiring your clients to come in yearly even though you're giving 3-year vaccines...